BN0536 Genetic Spatial Mapping Report

Genetic Spatial Mapping Plot

This plot shows the spatial genetic mapping results across different tissues.

Cauchy Combination Result

This table presents the results of the Cauchy combination test, summarizing the genetic associations.

Annotation P Cauchy P Median
Layer 3 4.7892e-05 3.1438e-03
Layer 2 7.7822e-05 1.1757e-02
Layer 4 3.7625e-04 4.4041e-03
Layer 5 7.7612e-04 2.3346e-03
Layer 1 8.7943e-04 6.7126e-02
Layer 6 1.5332e-03 6.6939e-03
WM 2.5246e-03 1.3976e-01

Diagnosis Manhattan Plot

The Manhattan plot shows the association of SNPs with the top associated gene across the genome.

Gene Expression and GSS Distribution

Select a gene to view its expression distribution and gene specificity score (GSS).

Expression Distribution
TUBB2A Expression Distribution
Gene Specificity Score (GSS)
TUBB2A GSS Distribution

Top 50 Gene Diagnostic Info

This table lists the top 50 genes based on diagnostic criteria, including the gene specificity score (GSS) and PCC.

Gene Annotation Median GSS PCC
TUBB2A Layer 5 2.7480 0.6112
COX6C Layer 2 2.2832 0.6101
SNAP25 Layer 5 2.5723 0.6075
UCHL1 Layer 3 2.2773 0.6065
CCK Layer 3 2.5000 0.6044
HSP90AB1 Layer 5 2.2930 0.6030
NEFL Layer 3 2.9219 0.6020
RTN3 Layer 5 2.5176 0.6018
ATP6V0C Layer 5 2.4785 0.6010
ATP5F1E Layer 5 2.1973 0.5992
NDUFA4 Layer 5 2.3594 0.5987
VSNL1 Layer 2 2.6309 0.5977
C9orf16 Layer 3 2.4570 0.5954
STMN1 Layer 5 2.4453 0.5948
RTN1 Layer 5 2.6895 0.5930
PPIA Layer 5 2.3281 0.5920
CHCHD10 Layer 5 2.4785 0.5919
CALM3 Layer 5 2.4082 0.5918
COX4I1 Layer 5 2.1875 0.5911
OAZ1 Layer 5 2.5332 0.5910
TUBA1B Layer 5 2.2422 0.5906
PCSK1N Layer 3 2.4727 0.5905
GNAS Layer 2 2.2578 0.5905
BASP1 Layer 5 2.7070 0.5901
SNCA Layer 5 2.6191 0.5894
EEF1A2 Layer 5 2.7012 0.5893
CHN1 Layer 5 2.7305 0.5888
SYP Layer 5 2.7656 0.5874
GPM6A Layer 2 2.2520 0.5873
TPI1 Layer 5 2.3398 0.5863
NDUFS5 Layer 5 2.3086 0.5861
HSP90AA1 Layer 5 2.3496 0.5859
NRGN Layer 2 2.3184 0.5857
SEPTIN3 Layer 5 2.4238 0.5844
DNM1 Layer 2 2.5898 0.5833
THY1 Layer 6 2.6484 0.5824
MGST3 Layer 5 2.6250 0.5807
CLSTN1 Layer 5 2.5000 0.5796
YWHAG Layer 5 2.6543 0.5795
UBB Layer 5 2.1348 0.5794
TSPAN7 Layer 5 2.3184 0.5786
SELENOW Layer 5 2.0781 0.5782
COX7C Layer 5 2.2871 0.5770
ATP1B1 Layer 5 2.4785 0.5766
PEBP1 Layer 5 2.3242 0.5757
PSAP Layer 2 2.2461 0.5754
YWHAH Layer 5 2.4082 0.5752
GRIN1 Layer 5 2.2578 0.5750
MAP1B Layer 5 2.6777 0.5748
BEX3 Layer 5 2.5000 0.5738

Running Info

Click to view detailed run information and parameters.

gsMap Version: 1.73.0

Parameters:

  • Sample Name: BN0536
  • Trait Name: PD
  • Summary Statistics File: /mnt/data/projects/ASAP/ST/gsMAP/GWAS_nallsEtAl2019_allSamples_allVariants.sumstats.gz
  • HDF5 Path: /mnt/data/projects/ASAP/ST/gsMAP/st_anndata_h5ads/st_adata_BN0536_for_gsmap.h5ad
  • Annotation: smoothed_label_s5
  • Spatial LDSC Save Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN0536/spatial_ldsc
  • Cauchy Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN0536/cauchy_combination
  • Report Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN0536/report/PD
  • gsMap Report File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN0536/report/PD/BN0536_PD_gsMap_Report.html
  • Gene Diagnostic Info File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN0536/report/PD/BN0536_PD_Gene_Diagnostic_Info.csv
  • Report Generation Date: 2025-04-11 00:25:20
  • Number of Processes: 10
  • Spending Time: 0h 3m